Interesting stuff.... but I am still confused. I too have the wrappers off of most cigars. Here is another (and quite different) perspective on cigar storage from the FAQ section of another popular web site that also seems to make intuitive sense.
Q: Should I leave the cellophane on or take it off?
A: Leaving the cellophane on protects the cigars from tattering and splitting while you handle them. Also, cellophaned cigars are easier to take “on the road" or send to friends.
Without the cellophane, cigars tend to breath better and, in turn, age better. Also, I find it much more appealing to open my humidor and see cigars in the nude.
Cellophane is permeable to water and air allowing their transfer through its surface, but not as easily as without the cellophane. So if I receive a batch of cigars that is freshly rolled, I sometimes remove the cello to allow the excess moisture incurred during the rolling process to dissipate. Cigars that become too moist in cellophane take a long time to dry out.
So as a general rule, I leave the cellophane on cigars stored loose in my bulk storage units or in their original boxes, but take it off when I place them in my desktop humidors.
Either way is appropriate, and in the end it is really just a matter of personal choice.
Q: Do cigars age in tubes?
A: Yes and no. Cigars seem to age some in the tubes, but mostly I think this is due to most tubes not having a true seal. In an absolutely sealed environment it is impossible for a cigar to have the necessary oxygen required for it to breath and age properly. You will note that on many tubes it mentions that a cigar will "remain fresh until opened" and, personally, I do not consider this an ultimately desirable goal. Tubes are great for protecting cigars for a few weeks - even months- outside of a humidor if they have a good seal. But if tubed cigars are to be kept longer and you wish to ensure that they age properly, I recommend you remove the end caps and place them in your humidor. With all of that said, I have smoked many tubos whose seals were intact for years and the cigars were quite tasty. But no matter what you do, always store tubed cigars in a humidor if you are going to have them for any substantial length of time, because most tube seals are not air-tight.
Q: Can I leave the cigars in the boxes as they age?
A: Absolutely. In fact, most collectors do. However, if the box is sealed with a plastic wrap you should remove this prior to placing the box in your cabinet, humidor, or Igloodor.
Q: Will my cigars "marry" if they are sitting side by side in my humidor without dividers or cellophane?
A: No. I understand the concept of marrying, and have witnessed claro cigars that have been slightly stained with oils from a dark, rich EMS cigar that was sitting beside it, but that was only after MANY years. Honestly, I do not consider the marrying of different cigars to be a problem for those who smoke from their humidors on a semi-regular basis.
I have been storing singles side by side for well over a decade with no impact whatsoever. Personally, I find the concept of marrying flavors between differing cigars to be an issue that "cigar wonks" banter about, but has little basis in reality and does not warrant any concern on your part. You have to keep in mind, when you read all the recent advice printed about cigars, that quite a bit of it is far too reaching and overtly scientific without cause.
I have kept a wide variety of smokes crammed together for long periods (5+ years) in my "smoke from someday" humidors without this ever occurring. My only concern would be to always keep flavored (i.e.. rum soaked, Acid, etc.) separate. Also, for long-term aging in quantity, I believe in leaving the cigars in their original boxes if possible.
Bottom line: the concept of cigar flavors marrying/blending is over hyped.
